Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 98KJ2

Calculation Name: 4B9X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4B9X

Chain ID: A

ChEMBL ID:

UniProt ID: Q99MV1

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2130749.51197
FMO2-HF: Nuclear repulsion 2052052.276735
FMO2-HF: Total energy -78697.235235
FMO2-MP2: Total energy -78922.587054


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:697:LEU)


Summations of interaction energy for fragment #1(A:697:LEU)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-9.083-1.9014.382-2.873-8.69-0.006
Interaction energy analysis for fragmet #1(A:697:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.060 / q_NPA : -0.052
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A699TRP00.013-0.0013.811-0.7631.220-0.021-0.873-1.0880.000
4A700THR00.0400.0196.2800.0920.0920.0000.0000.0000.000
5A701TRP00.0160.01210.013-0.016-0.0160.0000.0000.0000.000
6A702VAL0-0.019-0.01013.1870.0160.0160.0000.0000.0000.000
7A703GLU-1-0.892-0.93015.511-0.420-0.4200.0000.0000.0000.000
8A704PHE0-0.027-0.02018.2650.0260.0260.0000.0000.0000.000
9A705THR0-0.058-0.01422.0240.0050.0050.0000.0000.0000.000
10A706VAL00.025-0.01525.119-0.003-0.0030.0000.0000.0000.000
11A707ASP-1-0.935-0.96827.853-0.101-0.1010.0000.0000.0000.000
12A708GLU-1-0.845-0.91024.474-0.170-0.1700.0000.0000.0000.000
13A709THR0-0.057-0.03528.421-0.003-0.0030.0000.0000.0000.000
14A710VAL0-0.011-0.01724.7460.0020.0020.0000.0000.0000.000
15A711ASP-1-0.879-0.93528.104-0.114-0.1140.0000.0000.0000.000
16A712VAL0-0.028-0.01124.966-0.014-0.0140.0000.0000.0000.000
17A713VAL00.009-0.00325.2060.0150.0150.0000.0000.0000.000
18A714VAL00.0120.01225.247-0.016-0.0160.0000.0000.0000.000
19A715CYS0-0.0470.00421.3560.0060.0060.0000.0000.0000.000
20A716MET00.0000.00021.4900.0160.0160.0000.0000.0000.000
21A717MET0-0.026-0.03324.469-0.001-0.0010.0000.0000.0000.000
22A718TYR0-0.0100.00522.8820.0040.0040.0000.0000.0000.000
23A719SER0-0.060-0.03828.3320.0130.0130.0000.0000.0000.000
24A720PRO00.0390.00529.741-0.007-0.0070.0000.0000.0000.000
25A721GLY0-0.010-0.00529.473-0.001-0.0010.0000.0000.0000.000
26A722GLU-1-0.962-0.96823.582-0.225-0.2250.0000.0000.0000.000
27A723PHE0-0.003-0.00425.2310.0110.0110.0000.0000.0000.000
28A724TYR00.0090.01618.745-0.007-0.0070.0000.0000.0000.000
29A725CYS0-0.020-0.00621.9500.0240.0240.0000.0000.0000.000
30A726HIS00.0150.01118.744-0.004-0.0040.0000.0000.0000.000
31A727PHE00.039-0.00720.9430.0200.0200.0000.0000.0000.000
32A728LEU0-0.041-0.02121.885-0.007-0.0070.0000.0000.0000.000
33A729LYS10.8430.90520.6630.2280.2280.0000.0000.0000.000
34A730ASP-1-0.908-0.95619.879-0.201-0.2010.0000.0000.0000.000
35A731ASP-1-0.887-0.94920.389-0.127-0.1270.0000.0000.0000.000
36A732ALA0-0.0240.00418.960-0.004-0.0040.0000.0000.0000.000
37A733LEU0-0.003-0.01919.060-0.015-0.0150.0000.0000.0000.000
38A734GLU-1-0.905-0.93720.937-0.111-0.1110.0000.0000.0000.000
39A735LYS10.8840.92616.5250.1720.1720.0000.0000.0000.000
40A736LEU0-0.037-0.01415.016-0.021-0.0210.0000.0000.0000.000
41A737ASP-1-0.906-0.94516.657-0.191-0.1910.0000.0000.0000.000
42A738ASP-1-0.918-0.95917.911-0.122-0.1220.0000.0000.0000.000
43A739LEU0-0.090-0.04410.624-0.002-0.0020.0000.0000.0000.000
44A740ASN00.048-0.00714.228-0.039-0.0390.0000.0000.0000.000
45A741GLN0-0.0200.00615.6880.0070.0070.0000.0000.0000.000
46A742SER0-0.034-0.01713.6880.0250.0250.0000.0000.0000.000
47A743LEU0-0.030-0.0279.3670.0020.0020.0000.0000.0000.000
48A744ALA00.0160.02313.3320.0050.0050.0000.0000.0000.000
49A745ASP-1-0.908-0.95216.627-0.052-0.0520.0000.0000.0000.000
50A746TYR0-0.122-0.0737.9600.0520.0520.0000.0000.0000.000
51A747CYS0-0.064-0.02712.106-0.002-0.0020.0000.0000.0000.000
52A748ALA00.0020.02513.8980.0090.0090.0000.0000.0000.000
53A749GLN0-0.022-0.02014.1030.0300.0300.0000.0000.0000.000
54A750LYS10.9060.93516.639-0.043-0.0430.0000.0000.0000.000
55A751PRO00.0240.01314.3390.0120.0120.0000.0000.0000.000
56A752PRO00.0590.0289.9640.0340.0340.0000.0000.0000.000
57A753ASN0-0.055-0.00810.321-0.025-0.0250.0000.0000.0000.000
58A754GLY0-0.027-0.01411.1460.0200.0200.0000.0000.0000.000
59A755PHE00.0390.0235.0320.0270.0270.0000.0000.0000.000
60A756LYS10.9550.9798.727-0.010-0.0100.0000.0000.0000.000
61A757ALA00.0080.0028.185-0.029-0.0290.0000.0000.0000.000
62A758GLU-1-0.951-0.9868.383-0.187-0.1870.0000.0000.0000.000
63A759ILE00.0240.0138.538-0.078-0.0780.0000.0000.0000.000
64A760GLY0-0.0060.0008.850-0.036-0.0360.0000.0000.0000.000
65A761ARG10.8830.9603.468-0.3100.0070.009-0.055-0.2710.000
66A762PRO00.0230.0062.276-1.119-0.1911.719-0.499-2.1470.002
67A763CYS0-0.095-0.0353.920-0.1180.2540.006-0.104-0.2740.000
68A764CYS00.0070.0136.134-0.084-0.0840.0000.0000.0000.000
69A765ALA00.0350.0169.1150.0620.0620.0000.0000.0000.000
70A766PHE00.0000.00112.2480.0030.0030.0000.0000.0000.000
71A767PHE00.0120.01315.7630.0070.0070.0000.0000.0000.000
72A768SER00.002-0.02118.2880.0120.0120.0000.0000.0000.000
73A769GLY0-0.038-0.01821.7140.0120.0120.0000.0000.0000.000
74A770ASP-1-0.857-0.93220.999-0.168-0.1680.0000.0000.0000.000
75A771GLY0-0.042-0.00621.2770.0090.0090.0000.0000.0000.000
76A772ASN0-0.0030.00918.1730.0170.0170.0000.0000.0000.000
77A773TRP0-0.025-0.01512.594-0.011-0.0110.0000.0000.0000.000
78A774TYR0-0.030-0.01513.105-0.004-0.0040.0000.0000.0000.000
79A775ARG10.7450.8448.1960.6740.6740.0000.0000.0000.000
80A776ALA0-0.002-0.0098.3480.0680.0680.0000.0000.0000.000
81A777LEU00.0000.0097.086-0.127-0.1270.0000.0000.0000.000
82A778VAL0-0.034-0.0088.0100.1070.1070.0000.0000.0000.000
83A779LYS10.9150.95710.2990.3280.3280.0000.0000.0000.000
84A780GLU-1-0.929-0.98313.622-0.216-0.2160.0000.0000.0000.000
85A781ILE00.0050.00812.949-0.003-0.0030.0000.0000.0000.000
86A782LEU0-0.019-0.00416.4540.0100.0100.0000.0000.0000.000
87A783PRO0-0.002-0.01120.0810.0070.0070.0000.0000.0000.000
88A784SER0-0.029-0.01021.9600.0080.0080.0000.0000.0000.000
89A785GLY00.0100.01219.305-0.003-0.0030.0000.0000.0000.000
90A786ASN0-0.025-0.02017.9960.0010.0010.0000.0000.0000.000
91A787VAL0-0.002-0.01012.4120.0000.0000.0000.0000.0000.000
92A788LYS10.9420.98515.8480.2130.2130.0000.0000.0000.000
93A789VAL00.0180.00511.520-0.033-0.0330.0000.0000.0000.000
94A790HIS0-0.014-0.00612.7150.0220.0220.0000.0000.0000.000
95A791PHE00.0720.02112.242-0.071-0.0710.0000.0000.0000.000
96A792VAL00.0000.0049.6690.0410.0410.0000.0000.0000.000
97A793ASP-1-0.742-0.86012.671-0.528-0.5280.0000.0000.0000.000
98A794TYR0-0.004-0.01314.8810.0380.0380.0000.0000.0000.000
99A795GLY00.0320.01316.5760.0280.0280.0000.0000.0000.000
100A796ASN0-0.0240.00618.1670.0000.0000.0000.0000.0000.000
101A797VAL0-0.042-0.04116.984-0.036-0.0360.0000.0000.0000.000
102A798GLU-1-0.903-0.94317.330-0.175-0.1750.0000.0000.0000.000
103A799GLU-1-0.974-0.98817.603-0.160-0.1600.0000.0000.0000.000
104A800VAL00.0220.02114.8600.0080.0080.0000.0000.0000.000
105A801THR00.014-0.00417.416-0.003-0.0030.0000.0000.0000.000
106A802THR00.027-0.00214.766-0.013-0.0130.0000.0000.0000.000
107A803ASP-1-0.961-0.97114.293-0.081-0.0810.0000.0000.0000.000
108A804GLN0-0.055-0.01315.689-0.005-0.0050.0000.0000.0000.000
109A805LEU00.002-0.00410.531-0.039-0.0390.0000.0000.0000.000
110A806GLN0-0.004-0.0039.3390.0510.0510.0000.0000.0000.000
111A807ALA00.0060.0014.947-0.067-0.0670.0000.0000.0000.000
112A808ILE00.0370.0212.634-0.492-0.0350.730-0.210-0.977-0.001
113A809LEU0-0.009-0.0063.359-1.547-0.4710.096-0.450-0.722-0.003
114A810PRO00.041-0.0042.650-1.423-0.4380.661-0.265-1.3820.001
115A811GLN00.0390.0263.812-0.229-0.1790.0070.006-0.0630.000
116A812PHE0-0.011-0.0056.5390.0220.0220.0000.0000.0000.000
117A813LEU0-0.024-0.0172.537-1.514-0.5001.175-0.423-1.766-0.005
118A814LEU0-0.0350.0006.5670.0050.0050.0000.0000.0000.000
119A815LEU0-0.0050.0199.2250.0410.0410.0000.0000.0000.000
120A816PRO00.0680.04310.501-0.127-0.1270.0000.0000.0000.000
121A817PHE0-0.0210.0006.5470.0130.0130.0000.0000.0000.000
122A818GLN00.019-0.04212.1380.0780.0780.0000.0000.0000.000
123A819GLY0-0.0040.02015.3630.0490.0490.0000.0000.0000.000
124A820MET0-0.016-0.00215.395-0.020-0.0200.0000.0000.0000.000
125A821GLN00.0350.02418.6970.0100.0100.0000.0000.0000.000
126A822CYS0-0.072-0.04220.6950.0010.0010.0000.0000.0000.000
127A823TRP0-0.031-0.00922.9260.0000.0000.0000.0000.0000.000
128A824LEU0-0.009-0.00327.6730.0020.0020.0000.0000.0000.000
129A825VAL00.0360.02730.031-0.001-0.0010.0000.0000.0000.000
130A826ASP-1-0.925-0.97032.279-0.099-0.0990.0000.0000.0000.000
131A827ILE0-0.037-0.03134.1440.0080.0080.0000.0000.0000.000
132A828GLN0-0.044-0.02435.065-0.007-0.0070.0000.0000.0000.000
133A829PRO0-0.012-0.02035.2450.0040.0040.0000.0000.0000.000
134A830PRO00.0070.01738.0580.0020.0020.0000.0000.0000.000
135A831ASN0-0.025-0.01241.4460.0050.0050.0000.0000.0000.000
136A832LYS10.9530.95338.5300.0790.0790.0000.0000.0000.000
137A833HIS00.0140.01934.515-0.007-0.0070.0000.0000.0000.000
138A834TRP00.0900.03831.6640.0100.0100.0000.0000.0000.000
139A835THR00.0310.01936.397-0.001-0.0010.0000.0000.0000.000
140A836LYS11.0010.97035.2850.0950.0950.0000.0000.0000.000
141A837GLU-1-0.927-0.96337.827-0.073-0.0730.0000.0000.0000.000
142A838ALA00.0210.01737.7750.0000.0000.0000.0000.0000.000
143A839THR0-0.009-0.01532.555-0.004-0.0040.0000.0000.0000.000
144A840ALA0-0.012-0.00134.976-0.003-0.0030.0000.0000.0000.000
145A841ARG10.9270.96137.2890.0780.0780.0000.0000.0000.000
146A842PHE00.0420.02430.1730.0020.0020.0000.0000.0000.000
147A843GLN00.0230.00330.377-0.001-0.0010.0000.0000.0000.000
148A844ALA0-0.058-0.03234.2200.0000.0000.0000.0000.0000.000
149A845CYM-1-0.874-0.87336.862-0.085-0.0850.0000.0000.0000.000
150A846VAL00.0000.00731.3470.0000.0000.0000.0000.0000.000
151A847VAL0-0.0180.00131.919-0.004-0.0040.0000.0000.0000.000
152A848GLY0-0.038-0.01731.4280.0060.0060.0000.0000.0000.000
153A849LEU0-0.011-0.00231.8630.0080.0080.0000.0000.0000.000
154A850LYS10.9180.97630.1890.0990.0990.0000.0000.0000.000
155A851LEU0-0.033-0.00830.7540.0080.0080.0000.0000.0000.000
156A852GLN00.0140.00330.607-0.006-0.0060.0000.0000.0000.000
157A853ALA00.0080.00227.7170.0020.0020.0000.0000.0000.000
158A854ARG10.9650.99029.7450.1080.1080.0000.0000.0000.000
159A855VAL00.000-0.00524.521-0.002-0.0020.0000.0000.0000.000
160A856VAL0-0.019-0.01127.6120.0070.0070.0000.0000.0000.000
161A857GLU-1-0.923-0.96127.141-0.148-0.1480.0000.0000.0000.000
162A858ILE00.0130.02021.385-0.011-0.0110.0000.0000.0000.000
163A859THR0-0.058-0.03421.1450.0040.0040.0000.0000.0000.000
164A860ALA00.0170.00116.556-0.011-0.0110.0000.0000.0000.000
165A861ASN0-0.087-0.04815.854-0.039-0.0390.0000.0000.0000.000
166A862GLY00.0870.04518.1410.0220.0220.0000.0000.0000.000
167A863VAL0-0.046-0.00620.2680.0050.0050.0000.0000.0000.000
168A864GLY00.0420.02623.2750.0030.0030.0000.0000.0000.000
169A865VAL0-0.025-0.03526.1210.0050.0050.0000.0000.0000.000
170A866GLU-1-0.853-0.91728.822-0.102-0.1020.0000.0000.0000.000
171A867LEU0-0.0030.00128.7830.0000.0000.0000.0000.0000.000
172A868THR00.001-0.01632.6460.0090.0090.0000.0000.0000.000
173A869ASP-1-0.820-0.89934.883-0.089-0.0890.0000.0000.0000.000
174A870LEU0-0.024-0.02435.8630.0050.0050.0000.0000.0000.000
175A871SER0-0.028-0.00638.7630.0050.0050.0000.0000.0000.000
176A872THR0-0.039-0.01740.1630.0060.0060.0000.0000.0000.000
177A873PRO00.004-0.01842.917-0.002-0.0020.0000.0000.0000.000
178A874TYR0-0.080-0.02145.2890.0010.0010.0000.0000.0000.000
179A875PRO00.0170.00440.715-0.002-0.0020.0000.0000.0000.000
180A876LYS10.8160.85539.6570.0850.0850.0000.0000.0000.000
181A877ILE00.0220.01437.041-0.004-0.0040.0000.0000.0000.000
182A878ILE00.0180.00534.5340.0030.0030.0000.0000.0000.000
183A879SER00.040-0.00735.5650.0050.0050.0000.0000.0000.000
184A880ASP-1-0.870-0.94337.342-0.077-0.0770.0000.0000.0000.000
185A881VAL0-0.122-0.05240.1000.0060.0060.0000.0000.0000.000
186A882LEU00.0350.01936.0910.0030.0030.0000.0000.0000.000
187A883ILE0-0.0170.00239.7570.0030.0030.0000.0000.0000.000
188A884ARG10.8950.94142.5560.0720.0720.0000.0000.0000.000
189A885GLU-1-0.902-0.95743.166-0.071-0.0710.0000.0000.0000.000
190A886GLN0-0.073-0.03745.3120.0010.0010.0000.0000.0000.000
191A887LEU0-0.0020.01440.9350.0000.0000.0000.0000.0000.000
192A888VAL0-0.050-0.02337.329-0.004-0.0040.0000.0000.0000.000
193A889LEU0-0.0260.00740.1700.0050.0050.0000.0000.0000.000
194A890ARG11.0191.00739.5240.0710.0710.0000.0000.0000.000
195A891CYS0-0.031-0.00235.6970.0020.0020.0000.0000.0000.000
196A892GLY0-0.0220.00439.2070.0010.0010.0000.0000.0000.000